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- PDB-3qw3: Structure of Leishmania donovani OMP decarboxylase -

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Basic information

Entry
Database: PDB / ID: 3qw3
TitleStructure of Leishmania donovani OMP decarboxylase
ComponentsOrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative (Ompdcase-oprtase, putative)
KeywordsTRANSFERASE / LYASE / orotidine monophosphate decarboxylase
Function / homology
Function and homology information


orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / nucleoside metabolic process / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
Orotidine 5'-phosphate decarboxylase, type 2 / Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like ...Orotidine 5'-phosphate decarboxylase, type 2 / Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsFrench, J.B. / Ealick, S.E.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Leishmania donovani UMP synthase is essential for promastigote viability and has an unusual tetrameric structure that exhibits substrate-controlled oligomerization.
Authors: French, J.B. / Yates, P.A. / Soysa, D.R. / Boitz, J.M. / Carter, N.S. / Chang, B. / Ullman, B. / Ealick, S.E.
History
DepositionFeb 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative (Ompdcase-oprtase, putative)
B: Orotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative (Ompdcase-oprtase, putative)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,30911
Polymers54,4442
Non-polymers8659
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-148 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.377, 98.165, 62.137
Angle α, β, γ (deg.)90.000, 106.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Orotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative (Ompdcase-oprtase, putative)


Mass: 27222.049 Da / Num. of mol.: 2 / Fragment: unp residues 1-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LinJ16.0560 / Production host: Escherichia coli (E. coli)
References: UniProt: A4HWV2, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M ammonium sulfate 10 % dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2009
RadiationMonochromator: Cryo-cooled si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 62080 / Num. obs: 62080 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.064 / Χ2: 1.452 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.60.27758530.815193.5
1.76-1.834.10.21362060.991198.4
1.83-1.914.30.16161681.237198.7
1.91-2.024.30.12862451.345198.8
2.02-2.144.40.10862481.493199.1
2.14-2.314.30.0962281.569199.3
2.31-2.544.30.07762501.736199.5
2.54-2.914.30.06562901.745199.7
2.91-3.664.30.06163491.846199.9
3.66-504.20.04462431.544197.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.848 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3147 5.1 %RANDOM
Rwork0.1927 ---
obs0.1939 62077 97.71 %-
all-62080 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.51 Å2 / Biso mean: 22.1575 Å2 / Biso min: 11.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20.29 Å2
2---0.72 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 45 253 3978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223870
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9675275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2525511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65122.987154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58415573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1031529
X-RAY DIFFRACTIONr_chiral_restr0.0730.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212955
X-RAY DIFFRACTIONr_mcbond_it0.5721.52517
X-RAY DIFFRACTIONr_mcangle_it1.08823977
X-RAY DIFFRACTIONr_scbond_it1.54231353
X-RAY DIFFRACTIONr_scangle_it2.6354.51295
LS refinement shellResolution: 1.704→1.749 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 171 -
Rwork0.257 3687 -
all-3858 -
obs--82.03 %

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